Stephen "Stippo" Rakes, a key prosecution witness in the murder trial of alleged crime boss James "Whitey" Bulger, has been found dead, authorities said.

The body of Rakes, 59, had "no obvious signs of trauma" and an autopsy is being performed to determine the cause of death, Middlesex District Attorney Marian Ryan and Lincoln, Mass., Police Chief Kevin Mooney announced today.

The corpse was found on Mill Street in Lincoln yesterday at 1:30 p.m., police said.

The judge overseeing the Bulger case hunkered down with lawyers in a confidential conference at the South Boston courthouse today where the trial is being held. Bulger, alleged to be a notorious and murderous crime boss and federal informant, is standing trial after being found on the lam in California two years ago.

Federal prosecutors said Rakes was supposed to testify that Bulger and associate Stephen Flemmi threatened his daughter at gunpoint and forced him to turn over his South Boston liquor store, which became Bulger's headquarters. Bulger sidekick Kevin Weeks testified last week Rakes' contention that Bulger's gang put a gun to his daughter's head was bogus.

Rakes comes from a storied South Boston family. His brother Joseph Rakes was photographed in Stanley Forman's Pulitzer Prize winning photograph charging at an African-American man on Boston's City Hall with the sharp end of the American flag - which became the symbol of the racial unrest during the city's anti-busing crisis.

News of his death investigation came on the same day that Stephen "The Rifleman" Flemmi was slated to take the stand against Bulger. The two men ran the Winter Hill Gang for decades while also working as informants for the FBI, according to prosecutors and courtroom testimony.

Police told the Rakes family the death appeared to be a suicide. But a source close to the Rakes family told ABC News that "he had no phone, no wallet, and police are still looking for his car." The body of the man found in Lincoln was positively identified as Rakes this morning after a fingerprint match, sources said.

Rakes' longtime friend Steve Davis, whose sister Debbie was allegedly murdered by Bulger, had met him for breakfast daily before court. Davis said he last saw Rakes Tuesday in court but then couldn't reach him all night Tuesday and yesterday he did not meet him in the courthouse cafeteria for breakfast.

"Stippo would not kill himself. Absolutely not,'' Davis told ABC News this morning. "He was looking forward to taking the stand. He told me over and over he had a big bombshell to drop. He had everything to live for and was looking forward to his day in court."

Davis - who lost his sister, brother and father to homicide, and whose daughter was killed in a drunk driver accident - was devastated by the news.